Mitochondria play a key role in whole-body metabolism: a complex process involving many di&#64256;erent tissues, such as muscle, fat, liver, and pancreas, in an intimate relationship be- tween signaling pathways and metabolic networks. Mitochondrial dysfunction can result from several factors, including oxidative stress, which inhibit the ability of mitochondria to maintain the mitochondrial membrane potential Delta Psi. Emerging evidence supports the hypothesis that mitochondrial dysfunction causes insulin resistance and hyperglycemia: prominent features of type 2 diabetes. Such analyses have emphasized the critical roles of ROS, UCP, and mitochondrial density in disease progression. Although many of the details of mitochondrial ROS production and UCP regulation are still being unravelled experimentally, we developed a model based on the data and information currently available to test the current understanding and make predictions about the system. The model we developed goes beyond the models upon which it was based by incorporat- ing ROS production and the activity of SE and UCP. Importantly, it is capable of capturing the nonlinear behavior of the proton-leak rate as a function of membrane potential and UCP activity. The models simplicity is an advantage in that it allows easy manipulation and transference (i.e., through parameter adjustments), making it useful in pursuing research in- vestigating the integrative physiology of mitochondria. Having been developed for pancreatic beta-cell mitochondria, the model allows us to make inferences and propose hypotheses related to insulin secretion: results that may be relevant to complications presented in patients with diabetes and impaired glucose-stimulated insulin secretion. There are multiple limitations to the current model, such as: It does not include adaptive responses, such as increases in antioxidant levels in response to elevated ROS levels, that might occur in living cells. We only considered superoxide as the endogenous UCP activatior here, but other potential activators, such as other forms of ROS, such as hydroxynonenal, and fatty acids, have been identi&#64257;ed experimentally. Although the intracellular calcium level was held constant for the simulations presented, it would actually be expected to become elevated and experience bursts and oscillations in response to glucose (25), po- tentially exaggerating the results shown here, given the polarizing e&#64256;ects calcium has on mitochondria. We also neglected the Delta pH component of the proton motive force and the energization-dependent properties of ANT and other pathways in the proton leak rate, for reasons discussed in the Modeling methods section. These and more are all limitations, but each limitation can and will be addressed in future generations of the model. The current version of the model has many uses. The functional forms used to model ROS production, UCP regulation, and proton leak rates are important. Many details related to these mechanisms are still unknown in the experimental literature. We based the form of the ROS production &#64258;uxes on those of the NADH and FADH2 oxidation rates, and used sim- ple mass action relationships, without saturation, cooperativity, or other more complicated relationships, to model UCP production, activation, and decay. The fact that the model can match reasonably complex experimental data implies that the functional forms used contain enough detail, without requiring the burden of more complicated relationships, to capture the existing experimental observations within physiological ranges. In turn, these functional forms may provide useful insight and enhance experimental deductions. Model simulations were used here to examine the short- and long-term e&#64256;ects that per- turbations in UCP activity and mitochondrial density have on beta -cell function. Results predict that short-term inhibition of UCP will prevent the diversion of protons from ATP production and enhance ROS signaling. Such a response may improve glucose-stimulated insulin secretion (9). But long-term inhibition of UCP is predicted to cause a sustained increase in ROS levels, and would therefore be expected to cause persistent oxidative stress. By increasing the mitochondrial density within the cell, the metabolic load can be shared among more mitochondria, and it is predicted that this serves to increase the ATP/ADP ra- tio response to glucose while decreasing oxidative stress. Experimentally, the perturbations in UCP activity and mitochondrial density we discussed could potentially be accomplished using pharmacological UCP inhibitors, such as genipin, and activators of the sirtuin, SIRT1, which is a regulator of mitochondrial biogenesis, and the peroxisome proliferator- activated receptors-gamma coactivator, PGC1alpha, which is a transcriptional coactivator that controls mitochondrial biogenesis. The fact that common human diseases and changes in metabolic states are often associ- ated with relatively small changes in many enzymes, rather than two-fold or greater changes in only a few enzymes, illustrates the crucial importance of quantitative modeling in their investigation. The model presented here provides a way to test the current understanding of a complex system, and examine how perturbations may a&#64256;ect the system over time.